Please don't list this on a work's page as a trope. Examples can go on the work's YMMV tab.
Nightmare Fuel: The Beach Boys
The aborted Smile album had a few.
"The Old Master Painter" track begins with a brief string rendition of the aforementioned and then progresses to a haunting version of "You Are My Sunshine", which has its lyrics put to past tense (eg. "You were my sunshine...") and make it appear as a melancholic song about a person suffering from a heartbreak. It does not help that Dennis Wilson's vocals have been altered to have an echoey timbre. The song ends on a long descending note played on violins, as if it's meant to project the idea that the singer had either lost his mind or apparently committed suicide.
The instrumental outtake, "Look", opens with a stark and moody piano chord progression.
The original ending to "Surf's Up". Wordless vocals continue to go on until the song gradually fades.
A very notorious example would be the Fire section of The Elements Suite. While the piece was supposed to convey the Great Chicago Fire of 1871, Brian Wilson based the composition on his second LSD trip, wherein he experienced ego death and saw himself burning within the fires of hell. Roughly three minutes of this is purely screeching violins and organ jabs amidst the array of chaotic sound effects. If that is disturbing enough, what is more disturbing is the story of the recording itself. Unbeknownst to Wilson, at the time he was working on the Fire section, parts of neighboring Santa Monica were put to flames. Once word got to him, he was so convinced that the ordeal unleashed "bad vibrations", that he immediately halted work on this song. Eerie.
The Smiley Smile version of "Wonderful", in its sparse arrangement of piano and sustained organ, benefits from a sinister vocal turn by Carl Wilson (making what was a song about losing consensual innocence feel like a song about being an unsuspecting target of prowling rapist, making it all the more creepy). The seemingly-jovial interlude heightens the listener's fears. The whole song feels so somber and gloomy. Not something to Smile about.
The album's version of "Wind Chimes" is this, as well. It's unsettling enough that the song has a calm yet dark vibe, then once the last verse is about to end, there is a dissonant noise that blares out of nowhere. Could count as a middle note nightmare.
The fact that "Never Learn Not to Love" is a revised cover of a song written by a would-be murderer is already uncomfortable to start with.
"'Til I Die" immediately begins with a droning synthesizer chord progression that plays throughout the whole song. The song's themes of despair, anguish, and (of course) death further brings chills down the listener's spine.
All of Summer In Paradise qualifies. It's hard to believe that Mike Love could fathom such an album...but he did.
The intro to "Wouldn't It Be Nice" can be this for some. The carnival-like melody being played sounds just a little...off.